Just follow the following steps:
1. Select the file you want, plus the master file it belongs to;
2. Right-click the .esm file and select ‘Apply filter for cleanin’;
3. Right-click the .esm file and select ‘Remove “Identical to Master” records’;
4. Right-click the .esm file and select ‘Undelete and disable references’;
5. Close the program via the ‘X’. It will ask to save the changes to file. Make sure just the one file you have edited is displayed. Otherwise, unselect the once you did not clean.